


Down the Rabbit Hole

by Eff_Dragonkiller



Series: Impossible Things [1]
Category: Shadowhunters (TV)
Genre: 2021 Shadowhunters (TV) Rewatch, Alternate Universe - Canon Divergence, Discord: Malec Server, Episode: s01e01 The Mortal Cup, Fraywood Brotp, Gen
Language: English
Status: Completed
Published: 2021-01-08
Updated: 2021-01-08
Packaged: 2021-03-12 13:15:17
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,698
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28636110
Author URL: https://archiveofourown.org/users/Eff_Dragonkiller/pseuds/Eff_Dragonkiller
Summary: Clary arrived at the police station in time to catch Luke alone. And like any responsible adult, Luke prioritized her safety first. Except the only people he thought could protect her from the Circle, were also Shadowhunters.So Clary Fray's introduction to the Shadow World comes from Alec Lightwood, Acting Head of the Shadowhunters' New York Institute.
Relationships: Clary Fray & Alec Lightwood, Clary Fray & Luke Garroway, Clary Fray & Simon Lewis
Series: Impossible Things [1]
Series URL: https://archiveofourown.org/series/2098536
Comments: 20
Kudos: 175





	Down the Rabbit Hole

Clary had no idea what was going on. She stumbled out of the glowing swirling hole into the empty hall close to Luke's desk. Hurrying down the stairs as the click of heels came closer, Clary avoided being seen. What would she say if she was stopped? 'I know I'm not supposed to be here, but magic?'

Who would believe that? She didn't believe that! Magic, like something out of Alice in Wonderland. When had she fallen down the rabbit hole? Because she couldn't remember a time in her life that things had made less sense. Her mom had been keeping secrets. Dot and Luke knew what those secrets were. Which meant they had been keeping secrets from her, too. Magic was real, her Mom had kept it from her and something had gone wrong.

Really, really wrong, but Luke was here, and he'd be able to fix it.

Logically, in the part of her mind that wasn't focusing on looking calm, Clary knew that whatever was going on was likely larger than something Luke could fix with a couple of words, or even a couple of bullets, but she tried not to think about it. She didn't know what she would do if she lost her family. It was just her and her mom. Dot and Luke and Simon, she'd do anything for any of them. Whatever they needed, she would do it. Eyes glazing with tears, Clary scrambled through the desks in the bullpen, not even trying to be quiet.

"Clary? What's wrong?"

"Luke! Mom and Dot, they were- there were men with swords and this guy with tattoos and magic?! And they sent me here! Said that it wasn't safe!"

Something in that must have made sense, because Luke was already moving. One hand still on her arm as he holstered his weapon, grabbed his coat, his badge, and his keys, and began hustling her toward the garage. "We gotta go."

"Luke? I don't understand?"

"I know, Clary, but I need you to trust me. If they found your Mom and you, then they probably already know where to find me. We have to move."

She sucked in a trembling breath and worked hard at keeping up with Luke's pace. It sounded more and more like this wasn't a mistake. This wasn't a crazy prank or a- a drug induced hallucination. Not if Luke was reacting like this. Clary wanted answers. Her Mom and Dot were in danger, but she put her effort into quietly keeping up with the Detective. The faster they were somewhere he thought was safe, the faster she might get some answers.

Buckling herself in, Clary asked, "Where are we going?"

"Somewhere safe," Luke frowned, "which doesn't give us a lot of options at the moment. They were at the shop?"

"Yeah."

"Then we really don't have many choices," Luke said, turning his car east. "Between the house and my desk in the bullpen, they'll have many options to track us with."

"Track us?" That didn't sound good, "I can turn my phone off?"

"No, magic." He shot a quick glance, and Clary could only imagine what her face looked like because he grimaced and admitted, "This wasn't how your mother wanted you to find out. Hell, she'd have been happy if you never found out."

"Didn't matter, did it?" Clary snapped, biting her tongue because she knew her mother. Once Jocelyn Fray got her mind set on something, there wasn't a lot you could do about it. "That wasn't fair, I'm sorry."

"It's alright, kiddo." Luke sighed, offering a quick squeeze to her shoulder as they paused at a light. "I can't imagine what your night's been like."

God, had it only been a night? A check at the clock on the dash and she shook her head. It wasn't even midnight.

"It hasn't been good, that's for sure."

Luke pulled into the gravel lot of a pier-side church parking lot and cut the engine. "I know. Unfortunately, Clary, it's probably going to get worse."

"Explain it to me then. Mom and Dot need help and you've taken me to a church?" She turned in her seat to face him, "Shouldn't we be figuring out how to help?"

"They're stronger than you know," Luke offered. "If there's a way out, they'll manage it."

"They need help! We're family, we should help!"

"Clary, listen to me." Clary shook her head, reaching for the handle. Her mom needed help. Luke forcibly reached over and turned her around, "Listen to me! You don't know what you're getting yourself into! And I can guarantee that your mother would be far from happy with me if I brought you back into a fight she just sent you from!"

"But Mom-"

"She’s tough. Really tough," Luke said with a weak smile, "don't count her out yet."

"I just- she never-" Clary shook her head like the motion might shake her thoughts into order. "I don't understand. She's my mom. Why would she lie to me?"

Luke sighed. He pushed the hair from her face and pressed a kiss to her forehead. "Now, that's a long story, kiddo. But it's what I brought you here to talk to you about."

She wiped at the tears on her cheeks, took a deep breath and decided to be an adult. "Okay."

For a moment, the man she considered her father just watched her and the love in his eyes took her breath away. "God kiddo, I love you so much."

"I love you too, Luke." She swallowed another shuddering breath, "I'm just so scared for Mom."

He took a deep breath, "I'm scared too, but your Mom is tough. She's been through so much we never told you. Years and years ago, before you were even born, your mother and I were part of a group. A very dangerous group led by a very evil man. Under his direction we did things, Clary, that give me nightmares. We killed people, tortured them, threatened their families, the safety of their homes. They were innocent, and we wanted them dead just because they existed."

Clary bit her lip. That didn't sound like Luke or her Mom. They were the kindest, most accepting people she knew. But, well, maybe that was the point. Mrs. Cline's mother down the street had grown up a Nazi, and she let no one talk poorly about minorities while she was around. "What happened?"

"Your father's name is Valentine Morgenstern, and he hadn't always been evil." Luke winced at her gasp, "he'd been a charismatic man, your mother and I, and many others, met in school; chafing at the restrictions our government placed on us. He wanted to bring back the glory of our people."

Now it really sounded like Nazi rhetoric. Clary had so many questions. Luke talked about their victims like there had been hundreds of them, but she'd never heard anything about a group like this. He'd mentioned a government, but Clary didn't think he was talking about the United States. She was just so confused. But Luke was clearly fighting to tell her his story, so she promised herself she wouldn't interrupt without a good reason.

"See, your Mom and I, we're from a group of people called Shadowhunters and they sound like the good guys. They were created to serve a higher purpose. To protect humanity from demons. The founding families were blessed with drinking from the Mortal cup, the chalice that imbues mortals with angelic blood. With this supernatural gift, nephilim can use adamas—heavenly metal—to forge weapons and steles to burn angelic runes on their skin that give them supernatural strength and speed; all to hunt and kill the demons that slip between dimensions to hunt mortals."

"But you said they weren't good guys!" Clary blurted, clasping her hand over her mouth, but the words were already gone. That promise hadn't lasted long. "They don't sound like bad guys."

Luke offered her a sad smile, "I'm sure they don't think they are. Your mother and I never thought we were. But there are more types of people in the world than just Nephilim and Demons, Clary. And there are hundreds of years of history of oppression between Shadowhunters and the members of the Shadow world called downworlders. Shadowhunters are ruled by the Clave, and the Clave isn't a governmental body designed to be impartial. The Clave and the Consul, the ruler, are in place to ensure that Shadowhunters continue upholding the mission given to them by the angel Raziel. To kill demons. And often their interpretation includes anyone with demon blood, like warlocks, vampires, fae, and werewolves.

"Your mother, father, and I belonged to a group called the Circle. And under Valentine's leadership, your father's leadership, we wanted to exterminate the downworlders. All of them, law-abiding and innocent right along with the cruel and nasty. We didn't care."

"Why are you telling me this now?"

"Because the people that are after you and your Mom; they're the Circle and the only way to keep you safe is to contact the Clave." Luke cupped a hand around her face, "Kiddo, this is going to be so hard for you. But I need you to cooperate. It won't be fun. The Clave is awful, but you'll be safe. And if you're safe, then I can focus on finding your Mom. Alright?"

"Okay," Clary said, ignoring her tears as Luke pressed a kiss to her head. "I'll do my best."

"I know you will, Kiddo."

***

Alec considered whether being the Head of the Institute was really what he wanted to do with the rest of his life. Filing paperwork, reviewing reports, docking his parabatai's pay again—for incomplete reports and shoddy mission prep. Seriously. Was this what he wanted to do with the rest of his life?

"Boss?" Alessio ducked her head into the office, "We just got a tip from a Detective Garroway, he's a known werewolf. Says he has information about a resurgence of the Circle, but he's only willing to talk to the Head."

"He on the line?" Alec asked, already picking up the office phone as Alessio shook her head.

"No, sir." She stepped in to offer him a post-it note with a dockside address on it. "He asked you to meet him there as soon as possible."

It could be a trap, but Alec didn't think it was likely. The local wolf pack wasn't particularly civilized, but Garroway didn't have a record with the Clave beyond his existence. And if he'd made it as far as Detective, then he probably wasn't unhinged.

"You want back-up, Boss?"

"Yeah," Alec said. He tapped his pen against the desktop. "Jace on patrol?"

"He's not scheduled," Alessio said with a grimace, "but I don't think he's come back from your previous mission yet."

Alec sighed, "Awesome. Thanks, Ava."

"Sure thing, Boss."

Jace was his chosen brother, they'd bound their souls together in one of the most sacred rituals nephilim could take part in. Alec loved him. But Jace had all the reliability of a moody cat. One minute he was all smiles and hugs, 'sure, parabatai, anything for you'. The next he was breaking curfew, sneaking out at night, getting into fights, and skipping out on his duties as Alec's provisional second in command.

All of which boiled down to the fact that Jace wasn't here to leave the Institute too, and he wasn't here to be Alec's backup in the field.

"Grab Underhill and Darkwater for me?"

"Sure, Boss."

Isaiah Darkwater was the oldest active duty Shadowhunter, by at least ten years, in the world. At 48 he'd survived multiple wars between the downworld and the Clave, and at least three different Heads. As long as Darkwater continued to wipe the training salle of younger Shadowhunters, Alec was content to let him. It did however mean that the older man didn't quite heal up the way he used to.

"Alessio said you needed to see us, sir?" Underhill asked as he held the door open for Darkwater to hobble in on his crutches.

"I've been requested at a meeting about a resurgence of the Circle." Alec explained, gratified when both men took the news as seriously as he had. "Andrew, prepare a team to come with me, just in case. Isaiah, you're in charge until I'm back."

"Not Wayland?"

"No. Not Jace."

The church by the docks wasn't known to Alec, but it was hallowed ground and he could feel it as he approached. True worship was offered in this building, and it set Alec at ease. Even if it was a trap, the werewolf had chosen the worst location. Nephilim were more powerful on hallowed ground of true faith than anywhere else in the world.

"Father," Alec greeted the priest, "I'm meeting someone."

"They're at the front," the older man offered with a reverent smile. "Blessings on you, child."

"Angel's blessing on you, Father."

Well, it wasn't a trap. Luke Garroway had only brought one companion and considering the way she sat, head bowed and makeup ruined, this probably was official Institute business.

Angel, he hoped it wasn’t a rouge werewolf. Those hunts always ended up so bloody.

"Garroway?" Alec approached from a wide angle, his team setting up close enough to be back up but far enough away for plausible deniability. "You called about a resurgence of the Circle?"

Oh. Garroway had turned, and the edge of his collar had pulled away to show the upper half of a scarred rune. Garroway had been one of them.

"It's complicated," the man frowned. "I thought the Head of the New York Institute was Maryse and Robert Lightwood."

"I'm their son, Alec." He took a chance and seated himself on the pew in front of them. Uncomfortable, but not horrible. Difficult to defend, but not impossible. "I'm Acting Head while they're in Alicante."

Garroway nodded and turned his attention to the girl beside him, "This is Clary."

"Your daughter?"

He grimaced, "No, Valentine Morgenstern's."

Alec's breath caught in his throat and he settled a little further in his seat. "Why don't you start from the beginning?"

Which was how Alec learned that Garroway, Clary's Mom, and his parents were all founding members of the same terrorist group that had resulted in the deaths of thousands of downworlders and that was now hunting in New York.

"Valentine had begun to delve into experiments on other Shadowhunters, on their children—he had already killed one of his own children—when Jocelyn realized she was pregnant again, she ran."

"With the Mortal Cup?"

"Yes."

"Do you know where it is?" Alec asked after a moment.

"No, Jocelyn refused to tell me. Insisted it would be safer if no one else knew. Insisted we would be safer just as hidden, but-"

"But once Clary turned eighteen, it was only a matter of time." Alec sighed, this was complicated. So complicated. "Why come to the Institute? You know that as soon as the Inquisitor hears about this there will be hell to pay?"

"Who would I go to?" Garroway shook his head, "My alpha, who would sooner turn Clary over to Valentine than protect her; the vampires are the same—Camille Becourt is a serious piece of work. And the Warlocks? I admit, Jocelyn and I have some connection there, but they are already so few. They were hit hardest in the wars and have been held accountable for every evil deed that might have been done with warlock magic. High Warlock Bane would try to help, but I fear we would lead the Circle right to them instead."

If Garroway was correct in his reasoning, then the girl really was safest among the Shadowhunters.

Alec turned to Clary and just observed her for a moment, taking in all the ways she wasn’t anything like any of the women he knew. Her long hair was left unbound, dangerous among active duty Shadowhunters and shameful amongst their kin in Idris. Clothing and makeup were modest, not a single rune on any of the skin he could see, and Alec could tell from her hands she had never held a weapon in her life.

More than any of that, though, was her body language. She hunched in the pew. Her hair covered her face and her hands rubbed together again and again. Nervous ticks Alec would have to be blind not to notice.

He sighed, “What do you want?”

Her head jerked up, “What- what do you mean?”

“I don't know much about the way the mundane world works.” Alec admitted, “I was raised in the shadow world; everyone I know was raised in the shadow world. I held my first knife before I could walk, and could write my runes before the English alphabet. I know nothing else.”

When Clary said nothing and Luke didn’t interject, Alec continued. “Being a Shadowhunter is hard. We have an angelic mission, to protect the world from demons, but we're not always the good guys. You're going to do things you find gross and disgusting. There will be days you hate the job and maybe even hate yourself. Shadowhunters swear to uphold the law and the directives of the Clave - they're outdated, immoral, and will make you the villain in most of the downworld's perspective.” Alec said bluntly.

There was a time for careful words and tact, but it wasn’t now. Not from him.

“If you end up one of mine, I will do my best, my absolute best, to give you all the training and support you need to get through this. But I can't guarantee we'll be able to save your mom. I can't guarantee anything except that I'll do my best. So, what do you want, Clary Fray? Can you accept my protection knowing that I’ll keep you safe, but you have a tenth of the freedom you enjoyed as a mundane?”

Clary shook her head and wiped the tears from her cheeks, “What other choice do I have? To attempt to survive in the normal world? With those terrorists hunting me? Or the werewolves? Or vampires?”

Alec shrugged, “It might not be a good choice, but it’s still a choice.”

“Luke-”

“No, Clary,” Alec interrupted, “this needs to be your choice.”

She bit her lip and scooted forward on the pew. “Can you promise me something?”

“What?” Promises were dangerous things in the shadow world. Some held too much power, some didn’t hold enough.

“Promise me you’ll tell me the truth.” Clary’s gaze was intent, and for the first time Alec could see a potential in her that resonated. “Luke, Dot, my Mom, they all lied to me for years. It might have been for my good, but they were still lying. And now I have to trust that you’ll protect me. I just have to believe it? Promise me you’ll always tell me the truth.”

Alec considered the situation before nodding slowly, “I’ll promise that I will always tell you the truth as I know it, completely, so long as it does not interfere with the safety or the mission readiness of the Institute.”

She squinted, “I don’t know enough to see the loopholes in that.”

“I know,” Alec nodded, “but I have to think about more than just you. I have over a thousand Shadowhunters under my command. I’ve made them the same promise of support and safety that I’m making you. I can’t put you above them even for a moment.”

“He’s not wrong, Clary.” Luke offered from the side, “that’s a bit like Simon going up to the Chief of Police and demanding the names of undercover officers. It’s dangerous.”

Clary huffed, “Heavy is the head that wears the crown.”

“I’ll make this promise,” Alec offered with a small smile, “And in return you’ll promise me to always make your best effort to cooperate. You don’t have to like me, some days you’ll probably hate me, but I won’t be able to help you if you don’t cooperate.”

Biting her lip again—that was such an obvious tell—Clary gave an uncertain nod, but presented her arm when he reached for it. “I promise.”

“This really shouldn’t be your first rune,” Alec admitted as he reached for his stele. “But you’ll feel more comfortable if you know we’ll each keep our promises.” He hesitated before he drew, offering a quiet: “this is going to hurt.”

Alec pressed her arm next to his and over the skin of their joined forearms he drew the oathkeeper rune. Clary gasped at the pain and her eyes watered, but she didn’t tug her arm away once. She was made of sterner stuff than Alec had considered.

It wasn’t necessarily a bad thing.

“You probably need to get going.” Luke offered into the quiet, “the faster you get to the Institute the faster you’ll be safe from the Circle.”

“You’ll keep in touch, right?” Clary reached out to hug the man, holding tight with everything she had. “This isn’t goodbye forever, just for now.”

“More like ‘see you later’,” Luke said with a weak smile as the small group collected Alec’s team and headed out of the church.

“See you later,” Clary offered, staring after the man as he got in his car and drove away with barely a look behind him.

***

Running across the city was hard. Even with magic burning in her skin. Clary panted as she slowed to a walk outside the church Alec and the other Shadowhunter’s called the Institute. From where she stood it didn’t look so great, just another ramshackle building waiting to get torn down and replaced by expensive ultra-modern apartments.

“You can’t see it from there,” the woman of the small group said with a laugh. “Come on, come on. All you need is like ten more feet.”

Huffing, ten feet might as well be the summit of Mt Everest for all it felt possible right now, but Clary stumbled her way closer and oh god, the difference was amazing.

Rotten beams, crumbling stone, and broken glass turned into soaring spires of gothic arches. Crenelations curving from window ledges curved and fluttered like stone wings. The stained glass windows depicting scenes of angels and demons were so vivid it seemed possible they might step out of the glass and become real.

“Welcome to the Shadowhunters' New York Institute.” One man said, his smile was kind. “I’m Andrew Underhill, Head of Security, welcome home Clary Fray.”

She didn’t quite understand. There was something profound in the way Andrew spoke that Clary was only just getting the feeling of, but she smiled as she stumbled up the steps into the pale stone interior. The bright light, a harsh change.

“Don’t worry, you’ll get better,” the sole woman on the small team said with a grin. Lightly pushing Clary forward, “but in the meantime don’t stop unless you like muscle cramps.”

“Oh, yeah,” someone said as they passed some guards, “not fun.”

“Commander,” A gruff older man braced on a set of crutches greeted Alec from a bay of screens and desks, “Wayland’s back.”

“How’d it go?” Alec frowned. He reached out for the tablet offered, but didn’t stop. Instead, leading the way into an office close-by.

His office, Clary decided as she took in the piles of manila folders and tablets piled on the desk Alec leaned against.

“You should probably reach out to High Warlock Bane about damages.” The man said with a grimace, “Wayland was complaining about someone ‘getting in the way’.”

“Great. And I’ll probably be waiting for his After Action report until the Angel returns.” Alec sighed and he must have decided to deal with it later, because he drops the tablet on his desk and turns back to the group that followed him into the office. “Why don’t we do a round of introductions. Command, let me introduce you to our new foundling, Clary Fray. She’ll be undertaking training, but with who and on what is a conversation for tomorrow.” Alec frowned, “Everything should wait for tomorrow.”

They went around the room and offered their names, and Clary tried hard not to get flustered. The woman who’d herded her in was Ella Bridger. She had a darker complexion and hair such a vibrant blue Clary didn’t know how she hadn’t noticed outside. Andrew Underhill’s smile was just as patient and warm in the light as it had been outside in the dark.

The other woman was tall, pale, blond, and introduced herself as Marina Lutkivik. She had a thick accent that sounded a bit like Russian, but Clary wasn’t well traveled. She was probably entirely wrong. The older man on crutches introduced himself as Isaiah Darkwater, “not normally a member of Command. Not the Head of anything.”

“We’re missing a few,” Alec said when it came back to him. “But we’ll introduce you in the morning. Along with all the other urgent things we need set up. Where’s Wisebern?”

“It’s his day off,” Darkwater said gruffly, “Might have said something about Tahiti.”

Alec groaned and Clary watched as the small group chuckled and relaxed. She knew she wasn’t picking up on the subtext, but even she could tell that a level of tension had seeped from the others in the room.

“It’s okay, boss. Fray can stay with me. It’ll be like the kiddie dorms all over again.” Ella said, practically bouncing in place. “We can chat about knives and braids, it’ll be great.”

“Just for tonight,” Alec reassured her, “Wisebern will be back in the morning.”

“She’ll need to get papers from the Clave before he can assign her a space.” Andrew pointed out quietly, “Hopefully it will go smoothly, but-”

“Nothing ever goes smoothly with the Clave,” Alec finished, running his hands through his hair.

Ella just bumped her shoulder against Clary’s, “It’ll take as long as it takes. We’ll be fine.”

Alec eventually continued, mentioned something about explosions and his siblings—which didn’t sound terrifying at all—but Clary’s phone was ringing. It was Simon.

“Is it someone important?” Alec asked, startling her from close by. They were alone in the office, Marina leaving with a frown.

“My best friend,” Clary admitted, “I was with him earlier in the evening for my birthday. He might have dropped by the apartment or something.”

“Can you ignore it?”

“He’ll just keep calling. Or try to open a missing person’s report.”

“What could you say that’s the truth but mundane-acceptable?” Alec shrugged at her incredulous look. “The truth is always the easiest lie. If you make something up, then you have to remember what you said. Easy to get caught forgetting.”

“So the truth,” Clary fiddled with her phone. Simon was calling again. “I’m in protective custody?”

“Okay. Is he going to ask why?”

“Someone came after my mom,” Clary said, more certain. Just like Alec said, the truth but ...normalized. “She’s missing, and I’m in protective custody.”

“And you can’t tell him anything else.” Alec coached gently. “He could get in way over his head. It’s better if he doesn’t try to track you down.”

“Right.” Her voice wavered and tears pooled in her vision, “Will you stay? While I talk to Simon?”

“Clary? Clary, where are you? Are you okay? Your house, it’s on fire and there were bodies.”

The tears she’d been holding back wouldn’t stop and when she opened her mouth to speak she sobbed.

“Clary?!”

“Simon,” She choked out, accepting the box of tissues Alec offered as she curled in on the couch. “It’s horrible. Mom is missing!”

“Oh God, Clary, are you okay? Are you safe?”

“Luke- Luke got me to safety, but its protective custody. I can’t talk long.”

“Oh God, Fray. I’m so sorry. It’ll be okay, I promise. The police will figure it out. Your Mom will be safe.”

“I don’t know that she will, Simon.” Clary admitted softly, “I’m so scared.”

And even as Simon rambled reassurances in her ear, it was Alec’s tentative hug around her shoulders that made her feel safe. Everything was changing, but, Clary reassured herself, change didn’t have to be bad.

**Author's Note:**

> I will be following this canon divergence through all the Shadowhunters (TV) episodes. So, if you enjoyed this you might want to subscribe to the series.


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